Hannah Achtenberg Kinn, head of a taxpayer-funded Brooklyn nonprofit for autistic kids, rakes in almost $700,000 in salary and benefits, plus six weeks’ vacation — time often spent in the Hamptons pursuing her sideline as a landscape painter.

Her salary alone came to $403,142 in 2010, according to tax filings for the League School and the two related groups that make up the $26 million nonprofit. Kinn also got a $39,140 bonus and unspecified “other” compensation of $96,985.

Her total 2010 compensation package amounted to $683,233 with deferred compensation and pension, health and life-insurance benefits, the tax filings show.

Kinn’s salary and bonus alone put her outside the norm for executives of similar-size nonprofits who earned a median $265,005 in 2008, according to a 2010 report by watchdog group Charity Navigator.

“It’s outrageous,” fumed one staffer who said teachers at the League’s school program sometimes have to buy their own supplies. “I don’t know how she can justify it.”

Kinn was not seen at all in July at the Vanderbilt Street headquarters of the League Education & Treatment Center, according to the staff member.

But a spokesman for the nonprofit, who said Kinn was entitled to 30 days’ vacation, insisted she took only 10 days off in July.

Kinn’s Hamptons art studio was among those on a July tour put on by the Artists Alliance of East Hampton. She has sold her work at Hamptons and New York City galleries, and buyers include former President Bill Clinton, with whom she attended Oxford University.

Kinn, 67, has headed the nonprofit since 1979.

The organization provides services to kids with autism and other disabilities and to adults with developmental disabilities and psychiatric problems.

It is funded almost entirely by Medicaid, the state Office for People with Developmental Disabilities and the city Department of Education.

League spokesman Aron Bukspan defended Kinn’s pay, saying the board “relied upon an independent compensation-consulting firm to determine her compensation, which is comparable to directors at similar providers.”

Gov. Cuomo this year ordered state agencies to set guidelines for executive pay for health-care and social-service nonprofits that get state funding. The proposed regulations call for no more than $199,000 in state money to go to CEO pay and for agencies to apply for waivers if non-state money is used to exceed the salary limit.

“When these regulations have been finalized, the center and board will, of course, comply with them,” Bukspan said.